# paper-doc

A tool that supports the paper-writing process: it manages the materials,
sections, figures, and references that go into a paper. The name reflects the
document-centric core of the workflow — a paper is composed from structured
documents rather than written in one pass.

The first feature to land is the **template configuration**: a reusable library
of section fields plus named templates built from them, so that a paper is
written by filling in a known structure instead of deciding one.

The second is **paper authoring**: a paper is a document written against a
template, sentence by sentence, paragraph by paragraph. The structure is never
copied into the paper — it is read from the template on every render — so
switching a paper's template re-shapes the whole document in one write without
touching a single sentence.

## Tech Stack

**Backend**

- FastAPI (Python) — REST API
- SQLAlchemy + Alembic — ORM layer and schema migrations
- TiDB v8.5.0 — MySQL-compatible distributed SQL database, deployed in k3s
- MCP Python SDK — the same domain layer, exposed as MCP tools (see below)
- Dependencies managed with `venv` + `requirements.txt`

**Frontend**

- Vue 3 + Vite — single-page application
- `axios` — HTTP client
- `vue-router` — client-side routing
- `pinia` + `pinia-plugin-persistedstate` — state management with persistence
- Element Plus — UI component library
- Dependencies managed with `pnpm`

## Architecture

A decoupled SPA + REST API layout:

- The Vue SPA runs in the browser and talks to the backend exclusively over
  HTTP/JSON via `axios`. It holds no direct database access.
- The FastAPI backend owns all persistence. It connects to TiDB through
  SQLAlchemy sessions and owns the schema through Alembic migrations.
- TiDB runs inside the existing k3s cluster. The backend reaches it either
  through the in-cluster Service (`tidb-tidb.tidb:4000`) or, during local
  development, through the NodePort `192.168.1.88:32738`.

Development runs both parts locally: Vite serves the SPA with a dev proxy that
forwards `/api` to the FastAPI process, so the browser sees a single origin and
no CORS configuration is required.

```
Browser ──HTTP/JSON──▶ FastAPI ──SQLAlchemy──▶ TiDB (k3s)
   │                      ▲
   └── Vite dev server ───┘  (proxy /api)
```

## Domain Model

Six tables. Every one is prefixed with the module it belongs to, and a model
class is named after its table, so the schema can be read as three groups:

```
template_field_library            the 字段库: reusable headings
  id, name, level, font_size, font_color

template                          a named outline (模板)
  id, name, abstract

template_field                    a field placed in a template — and the only
  id, template_id → template,     home of display order
  field_id → template_field_library, sort

paper                             the document
  id, title, template_id, author, status, keywords, target_journal

paper_sentence                    one sentence, at one position, in one paper
  id, paper_id → paper, template_id, paper_template_filed_sort, sort, content

paper_sentence_reference          the citations of one sentence
  id, sentence_id → paper_sentence, reference_id, quote, sort
```

`paper` has no `abstract` column, and that is a decision rather than an
omission. A paper's abstract *is* a paragraph of its body — the template's
`0 Abstract` field — so it has a position in the document, the heading and
typography the template gives it, and the same sentence-by-sentence editing as
every other paragraph. A column for it would be a second home for the same
text, one the document never reads: a paper could show two different abstracts,
and the one in the column could drift from the one in the body. Revision
`a83f5c21d7b6` removed it, moving each stored abstract into the abstract
paragraph first.

`template_field` and `template_field_library` are one word apart and mean
opposite things. The first is a *placement* — this template puts this field
here, `sort` included. The second is the *catalogue* the field was picked from,
shared by every template and owned by none. The library is managed from the
模板 menu, because it is the raw material a template is built out of.

### The field library is flat, not a tree

`template_field_library` has no `parent_id`. Hierarchy is expressed only by `level`
(1 for `1.`, 2 for `1.1`), which is a *rendering hint*: it drives indentation
and numbering semantics in the UI and nothing else.

The reason is reuse. With a parent pointer a level-2 heading would belong to
exactly one level-1 heading, so "Background" could not sit under both
`1. Introduction` and `2. Related Work`. Flat fields are attached to templates,
not to each other, so one field can appear in any number of templates, in a
different position in each.

The numbering a reader sees is part of `name` and is written by the user
(`"1. Introduction"`, `"0 Abstract"`). Nothing derives or rewrites it.

### Display order lives in the join table

`template_field.sort` is a plain ascending integer and is the **only** thing
that decides what order a template's fields appear in. The order the user
clicked fields in is never stored, so selecting `字段1, 字段2.1, 字段2, 字段1.1`
and setting sorts `1, 4, 3, 2` renders as `字段1, 字段1.1, 字段2, 字段2.1`.

Two consequences are deliberate:

- **There is no unique constraint on `(template_id, field_id)`.** Placing the
  same field twice in one template is a legitimate layout — the same level-2
  heading under two different level-1 headings. The UI warns about a repeat; it
  does not forbid one.
- **Ties are legal.** Equal `sort` values are broken by insertion order, so the
  ordering is always total and stable. The UI warns about ties too, and offers a
  button that renumbers the selection `1..N`.

### Templates hold references, not copies

`template_field` points at a library field; it does not snapshot its name or
typography. Renaming or restyling a field therefore updates every template that
places it, which is what makes "fix the template and the section names follow"
work.

### A sentence is addressed by position, not by field id

`paper_sentence.paper_template_filed_sort` holds the `sort` of the template
placement the sentence belongs to — **not** `template_field.id`, and not
`template_field_library.id`. Together with `sort`, the sentence's own position inside
that paragraph, it is everything needed to place a line of text.

The indirection is the feature. Two templates have no rows in common, but they
can share a position, so a sentence that remembers "I sit at position 7" lands
on whatever the new template puts at position 7 when the paper is switched. The
alternative — pointing at a placement row — would make every sentence belong to
one template and turn a switch into a re-mapping of every line.

Three behaviours fall out of that one choice:

- **The structure exists before the content.** A paragraph is any position the
  template defines *or* any position a sentence occupies, so an unwritten
  paragraph still renders, empty, and a paper created a second ago already has
  its full shape.
- **A switch destroys nothing.** Positions the new template does not define are
  still rendered, in their place in the order, under the heading 未设定. Switch
  back and the old headings return, because the sentences never moved.
- **Ties and gaps are fine.** Sentences may share a `sort` (broken by `id`) and
  may be numbered `10, 20, 30` to leave room, exactly as `template_field.sort`
  allows.

The name `paper_template_filed_sort` keeps the spelling the feature was
specified with; it is the template field's `sort` (the `sort` column of
`template_field`). `paper_sentence.template_id` is the template the sentence was
written against. It is kept in step with the paper's current template and is
provenance rather than a lookup key: rendering never filters on it, which is
precisely why content survives a switch.

### A sentence is a line, not parsed text

Nothing in the writing path splits text. There is no sentence detector, no
punctuation rules and no comma handling: **one line in the editor is one
sentence**, and what the writer types is what is stored, minus runs of
whitespace (leading, trailing, and any newline pasted inside a line, which fold
to a single space so a sentence really is one line). Commas never break
anything — the only place a comma separates anything in this project is the
keyword field.

That is deliberate. A splitter that guesses wrong corrupts content, and the
guess would have to be right for every abbreviation (`et al.`, `i.e.`), every
decimal (`3.14`), every numbered list and every language the tool is used in.
The writer decides where a sentence ends; the software only decides what goes at
the seam between two of them.

Exactly one split has ever been performed, in revision `a83f5c21d7b6`, to move
the old `paper.abstract` column into the body. It cut *after* a Chinese full
stop (`。`) and nothing else — deliberately conservative: an English abstract
survives that migration as a single row rather than being cut at the first
`et al.`, and one long line is a line the writer can split by hand.

#### What goes at the seam

A paragraph is printed by concatenating its sentences in `sort` order, so the
seam between two of them has to be spelled out:
`app.crud.paper.sentence_separator` returns `""` or a single space, and the
document response carries it as `SentenceRead.separator_before`.

| Seam | Separator | Why |
|---|---|---|
| `……缺口。` + `本研究……` | `""` | Chinese needs nothing; the full stop separates |
| `First sentence.` + `Second.` | `" "` | without it the two print as `First sentence.Second.` |
| `缺口。` + `This study` | `" "` | mixed text takes the space |
| `test.` + `本研究……` | `" "` | same, in the other direction |
| anything + an empty sentence | `""` | an empty line carries citations, not text |

So the rule is about the seam rather than the language: a space goes in unless
**both** sides are CJK, where adjacency is already the convention. It is derived
on every read and never stored — a stored separator is one that can go stale
against the text it separates — and a client prints `separator_before +
content` and adds no spacing of its own.

`separator_before` was added because the alternative was already a bug: CJK
sentences printed correctly by accident (the full stop hides the missing space),
so nothing looked wrong until the first English paper, whose sentences would
have run together.

### Citations are a table, not a column

One sentence may quote several references, so
`paper_sentence_reference` holds one row per citation. `quote` — 引用内容 — is
required and must not be blank: a citation that does not say what it quotes is
rejected with `422` rather than stored as a half-record. `reference_id` is a
plain nullable integer with **no** foreign key, because the reference library
does not exist yet; a citation may therefore be written now and linked later.

### Foreign keys are declared, and this cluster enforces them

TiDB parses `FOREIGN KEY` for compatibility, and from v6.6 honours it when
`tidb_enable_foreign_key` is on. On the cluster this project runs against it is
on, so the constraints are real integrity rather than documentation: a dangling
insert is rejected (`1452`) and `ON DELETE CASCADE` / `SET NULL` actually fire.
Two consequences are worth knowing before touching a migration:

- **Tables must be created in dependency order**, and a rename must be checked
  rather than assumed. `RENAME TABLE` does carry a referencing constraint along
  with the renamed table here (the rename in revision `f27a1c6d9e04` was
  rehearsed against the cluster before it was written), but that is a property
  of the deployment, not of SQL.
- **The API still checks first.** A database violation surfaces as a generic
  driver error, while the application refuses with a message that names the row
  and the count:
  - deleting a library field still placed in a template → `409`, naming the
    field and how many templates use it;
  - deleting a template a paper is written against → `409`, naming the template
    and how many papers use it — the template *is* that paper's structure, so
    removing it would empty the paper rather than tidy up;
  - creating a template that references a missing field → `400`, and creating
    or patching a paper that references a missing template likewise.

The ORM cascades stay as well. `Template.items`, `Paper.sentences` and
`PaperSentence.citations` use `cascade="all, delete-orphan"`, so deleting a row
removes its dependents whether or not the database would have done it too —
which keeps behaviour identical on a cluster with foreign keys switched off.

## API

All routes are mounted under `/api`. Interactive docs at `/docs`.

| Method | Path | Notes |
|---|---|---|
| `GET` | `/health` | liveness plus a TiDB probe |
| `GET` | `/template-field-library` | `keyword`, `level`, `page`, `page_size` |
| `POST` | `/template-field-library` | create a library entry |
| `GET` `PATCH` `DELETE` | `/template-field-library/{id}` | read / partial update / delete |
| `POST` | `/template-field-library/batch-delete` | body `{ "ids": [...] }` |
| `GET` | `/templates` | `keyword` matches name **or** abstract |
| `POST` | `/templates` | name + abstract + ordered `fields` |
| `GET` `PATCH` `DELETE` | `/templates/{id}` | `PATCH` with `fields` replaces the selection |
| `POST` | `/templates/batch-delete` | body `{ "ids": [...] }` |
| `GET` | `/papers` | `keyword` matches title/author/keywords, plus `status`, `template_id` |
| `POST` | `/papers` | title + template + author/status/keywords/journal; no sentence rows are created |
| `GET` `PATCH` `DELETE` | `/papers/{id}` | `PATCH` with `template_id` **is** the template switch |
| `POST` | `/papers/batch-delete` | body `{ "ids": [...] }` |
| `GET` | `/papers/{id}/document` | the whole paper: paragraphs in order, citations, warnings |
| `GET` | `/papers/{id}/paragraphs/{sort}` | one paragraph, assembled as the document renders it |
| `PUT` | `/papers/{id}/paragraphs/{sort}` | full replacement; optional `target_sort` moves it |
| `POST` | `/papers/{id}/sentences` | append one sentence |
| `PATCH` `DELETE` | `/papers/{id}/sentences/{id}` | edit or remove one sentence |

Conventions worth knowing:

- `font_color` is stored and returned as canonical `#RRGGBB`. The API also
  accepts `rgb(r, g, b)`, `#rgb` and bare `aabbcc`, and normalises them on write.
- `font_size` is a JSON number, not a string — a client should not have to parse
  it before using it in a CSS rule.
- List endpoints return `{ items, total, page, page_size, pages }`.
- A template read returns `fields` already ordered by `sort`; clients never sort.
- Route paths mirror table names one for one: `/templates` for `template`,
  `/template-field-library` for `template_field_library`, `/papers` for
  `paper`.
- A paper document returns its `paragraphs` in ascending position order,
  already carrying their sentences and citation numbering. The client sorts
  nothing and merges nothing: two implementations of the same ordering rule
  would eventually disagree.
- Sentence `content` is folded to a single line (leading, trailing and inner
  whitespace runs collapse to one space), so an all-whitespace sentence becomes
  the empty string — legal, and rendered as a blank line. A citation with a
  blank `quote` is refused with `422`.
- `keywords` is stored as a canonical ``, ``-joined string; `，`、`;` and `；`
  are accepted on write and de-duplicated.
- Paper `status` is one of `draft`, `writing`, `done`.

## MCP server

The same domain layer is also served over the **Model Context Protocol**, so an
agent — Claude Code, Codex, the DeepSeek Harness — can write a paper without a
browser. Full manual: [docs/MCP.md](MCP.md).

It is a third front door rather than a second implementation. The REST routes,
the MCP tools and the seed script all call `app.crud` and all validate through
`app.schemas`, so a rule fixed in the CRUD layer is fixed everywhere and a paper
written by an agent is indistinguishable from one written by hand. What
`app/mcp/` adds is only what a *model* needs and a browser does not:

| Addition | Why the REST shape is wrong for a model |
|---|---|
| 29 tools with `paper_` / `paragraph_` / `sentence_` / `template_` / `field_` prefixes | a model picks a tool out of a list by its name, not by reading 29 descriptions |
| JSON strings, `None`-free, no pagination envelope on reads | a tool result is paid for in context tokens |
| `paragraph_write` addressed by **heading** as well as position | nobody writing "1. Introduction" knows the template places it at `sort = 20` |
| `paper_write` / `paper_write_text` | "generate the paper, then put it in" is one intention, not thirty round trips |
| `paper_delete` refuses once before it deletes | a cascading delete has no undo in a tool call |
| `sentence_search` across papers | the job is consistency — one paper says 洪水损失, the next must not say GUL |

Two transports are served from one build: `stdio`, which is what a client
spawns, and `streamable-http`, which is what a client on another machine
connects to (behind a bearer token). The package is split so that only
`app/mcp/server.py` knows a transport exists:

```
app/mcp/
├── server.py      transports, CLI, and the instructions sent at initialize
├── support.py     sessions, JSON shaping, heading resolution, the one text splitter
├── specs.py       the shapes a model may send (a paragraph, a sentence, a citation)
├── selfcheck.py   --check: connect once and print the tool surface
└── tools/         papers, paragraphs, sentences, templates, fields — registered
                   by register_all(), each tool three lines around an app.crud call
```

Two decisions are worth knowing before adding a tool. **Results are registered
with `structured_output=False`**: inferred from a `-> str` annotation, the SDK
publishes a `{"result": …}` envelope and sends the JSON twice, once as
`structuredContent` and once as text, and clients that read only one of the two
then disagree about what the tool returned. And **the docstring is the tool
description verbatim**, sent with every request — so a tool docstring is one or
two lines and the reasoning goes in the module docstring, where it costs
nothing.

## Frontend

### Shell

```
┌───────────────────┬──────────────────────────────────────┐
│ [mark] paper-doc  │  论文   模板                    [mk] │  header
├───────────────────┼──────────────────────────────────────┤
│  论文             │                                      │  second-level
│   论文列表        │  <RouterView>                        │  menu, left
│   新建论文        │                                      │
│   ── 我的论文 ──  │                                      │
│   ● 论文标题 A    │                                      │
│   ● 论文标题 B    │                                      │
└───────────────────┴──────────────────────────────────────┘
       <- 208px ->
```

The mark appears at both ends of the header. The second-level menu sits on the
**left** and is driven by `route.meta.section`, so a route declares which menu
it belongs to and deep links render correctly on first paint. Routes without a
`section` (the welcome page) show no menu.

The 论文 menu is the one that is not a static list: it carries the papers
themselves, read from the `papers` store, so a paper can be opened straight from
the rail. Every page that creates, renames or deletes a paper reloads that
store, which is what keeps the rail and the table showing the same thing. A
filter box appears once there are more than six papers.

Two things about this layout are deliberate and easy to break by accident:

- **Which side the menu lands on follows from its DOM order** inside the flex
  row in `App.vue` — first child, left. Moving it is a one-block change there,
  not a stylesheet override.
- **The logo block is exactly as wide as the rail.** Both read `asideWidth()`
  from `src/layout.ts`, so they cannot drift apart, and collapsing the rail
  narrows the logo block with it (dropping the wordmark and centring the mark).
  The header's own padding is zeroed for this; the two insets come from
  `ASIDE_INSET` so the mark lines up with the section title below it.

The column also carries through to the content: the rail is 208px and both the
top nav's first item and `.el-main` are inset a further 20px by their own
Element Plus defaults, so the menu text, the page body, and the page header all
start on the same vertical line.

### Shell metrics

`src/layout.ts` is the single source for the rail's width and inset. It is a
module rather than CSS custom properties because `el-aside` takes its width
through a prop, which would otherwise fight an inline style coming from the
stylesheet.

### List pages fill the window

A table is the page. Left alone it is as tall as its rows, so on a large screen
most of the window sits empty below the last row while the *page* is still the
thing that scrolls — the wrong half of the screen moving for a list that should
simply show more. The three list pages (`/papers`, `/templates/list`,
`/templates/fields`) therefore stretch the table to the height the window
offers, with the toolbar above it and the pagination below it staying put while
the rows scroll inside the table.

It is CSS only — no resize listener, no measured pixel height, nothing to go
stale when the rail collapses or the window changes. Four links carry it, and
each one is load-bearing:

| Piece | Why |
|---|---|
| `.page--fill` | `min-height: 100%` of the content area — a floor that still grows |
| `.card--fill` | makes the card a column so its body can pass the height down |
| `.card--fill > .el-card__body` | a column with `min-height: 0`, without which a flex child refuses to shrink below its content |
| `.table-fill` + `height="100%"` | `flex: 1 1 0` so the table takes the leftover height instead of claiming its content height as its basis; Element Plus then pins the header and scrolls the rows |

Measured in a real browser at three window sizes, with rows to scroll and with
none:

| Window | Table | Page scroll | Rows scroll | Empty state |
|---|---|---|---|---|
| 1920x1080 | 781px | none | 519px inside | centred, 741px |
| 1440x900 | 601px | none | 699px inside | centred, 561px |
| 1280x620 | 321px | none | 979px inside | centred, 281px |

`.table-fill` keeps a 240px floor. Below it — a 1280x420 window — the table
stops shrinking, the page grows past the viewport and the content area scrolls,
which is the pre-existing behaviour rather than a squashed table. Pages that
are not lists (the paper document) keep scrolling normally.

### Routes

| Path | View | Section |
|---|---|---|
| `/` | welcome | — |
| `/papers` | paper table + CRUD (`?new=1` opens the create dialog) | `papers` |
| `/papers/:id` | one paper, read as a document | `papers` |
| `/templates` | redirects to `/templates/list` | — |
| `/templates/list` | template table + CRUD | `templates` |
| `/templates/fields` | field library + CRUD | `templates` |

### The paper view

`PapersView` is the library; `papers/PaperDetailView` is the writing surface.
The detail view renders the server's document verbatim and adds three things it
alone knows how to do:

- **an edit button beside every paragraph**, written or not — content only ever
  enters a paper through the paragraph editor, so it may never be the thing that
  is missing;
- **numbered citation markers** in the text, matching the 参考文献 list, which
  is numbered in reading order rather than per paragraph;
- **a 切换模板 dialog that previews the impact** — how much content lands under
  a new heading, how much keeps its place under 未设定, and how many empty
  paragraphs the new template adds — because a switch re-shapes the whole
  document in one write.

Changing a paper's template from the metadata form is deliberately disabled: a
silent re-shape of the document is exactly what the preview exists to prevent.

## Directory Structure

```
paper-doc/
├── backend/                 # FastAPI application
│   ├── app/
│   │   ├── api/routes/      # route handlers (health, papers, templates,
│   │   │                    #   template_field_library)
│   │   ├── core/            # settings and configuration
│   │   ├── crud/            # data-access helpers
│   │   ├── db/              # engine, session, declarative base
│   │   ├── mcp/             # MCP server: tools, specs, transports, self-check
│   │   ├── models/          # SQLAlchemy models
│   │   └── schemas/         # Pydantic request/response models
│   ├── alembic/             # migration environment and revisions
│   ├── scripts/seed.py      # idempotent seed for the field library + templates
│   ├── scripts/smoke_papers.py  # end-to-end check of the writing loop
│   ├── scripts/mcp_server.py    # MCP entry point (stdio / http)
│   ├── scripts/smoke_mcp.py     # the same loop, spoken over MCP by a real client
│   ├── alembic.ini
│   ├── requirements.txt
│   └── .env.example
├── frontend/                # Vue 3 SPA
│   ├── src/
│   │   ├── api/             # axios instance and endpoint modules
│   │   ├── components/      # shell, field, template and paper components
│   │   ├── router/          # vue-router configuration
│   │   ├── stores/          # pinia stores (UI prefs persisted, the paper list not)
│   │   ├── styles/          # global reset and the shell viewport contract
│   │   ├── utils/           # formatting helpers
│   │   └── views/           # route-level components (papers/, templates/)
│   ├── package.json
│   └── vite.config.ts
└── docs/                    # project documentation
    └── OVERVIEW.md
```

## Getting Started

**Prerequisites**

- Python 3.10+ with `venv`
- Node.js 18+ with `pnpm`
- Network access to the TiDB instance (local development uses the NodePort)

**Backend**

```bash
cd backend
python3 -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt
cp .env.example .env          # then fill in the database credentials
uvicorn app.main:app --reload --port 8000
```

API docs are then served at <http://127.0.0.1:8000/docs>.

**Frontend**

```bash
cd frontend
pnpm install
pnpm dev
```

The SPA is served at <http://127.0.0.1:5173> and proxies `/api` to the backend
on port 8000.

**Database**

The `paper_doc` database is created once, out of band, against TiDB. Schema
changes are applied through Alembic:

```bash
cd backend
alembic upgrade head
```

**Seed data**

`scripts/seed.py` fills the field library with a standard academic outline (20
fields, from `0 Abstract` to `7 References`) and creates three starter
templates. It matches fields and templates by name, so running it twice adds
nothing:

```bash
cd backend
.venv/bin/python scripts/seed.py            # add anything missing
.venv/bin/python scripts/seed.py --reset    # empty the tables first
```

**Checking the paper feature end to end**

`scripts/smoke_papers.py` walks the whole writing loop against a running API —
create a paper on a template, verify the empty structure, fill a paragraph with
sentences and citations, switch the template, check that unmatched positions
survive under an unset heading, move a paragraph, and delete it all again. It
exits non-zero on the first failed expectation and cleans up after itself:

```bash
cd backend
.venv/bin/python scripts/smoke_papers.py
```

**Checking the MCP server**

`scripts/mcp_server.py --check` connects to the database once and prints the
tool surface, which is the failure this catches: a client that spawned the
server successfully and then sees every call fail. `scripts/smoke_mcp.py`
drives the whole writing loop through a real MCP client — the same child
process and JSON-RPC over stdin/stdout that Claude Code, Codex and the Harness
use — and runs unchanged against `--url` for the HTTP transport:

```bash
cd backend
.venv/bin/python scripts/mcp_server.py --check
.venv/bin/python scripts/smoke_mcp.py
```